Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ESR1

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF7 cell line
esr1 genotype
Wild-type
treatments
Vehicle
chip antibody
ERα (Santa Cruz Biotechnologies, sc543)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and ER-bound DNA complexes were isolated with antibody (Santa Cruz, sc-543). ChIP was performed according to our in-house protocols. A minimum of 10ng DNA was sent to McGill University sequencing core. The library was prepared using TruSeq ChIP Library Preperation kit (Illumina) and was sequenced on Hiseq 2500 (Illumina). Over 16M single end 50bp reads were allocated for each sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
23445317
Reads aligned (%)
86.3
Duplicates removed (%)
4.3
Number of peaks
647 (qval < 1E-05)

hg19

Number of total reads
23445317
Reads aligned (%)
85.5
Duplicates removed (%)
5.7
Number of peaks
885 (qval < 1E-05)

Base call quality data from DBCLS SRA